[merge] dev

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    environment: 
+    environment:
      name: testing
     strategy:
       matrix:

.vscode/settings.json

@@ -10,4 +10,4 @@
     ],
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
-}
+}

CHANGELOG.md

@@ -1,5 +1,46 @@
 # Change log
 
+## v0.4
+
+### Main changes
+
+- New `SequencingData` class to handle sequencing data
+- GUI can now be used to add data to flexilims with `flexiznam gui`
+- Add a `conda_envs` field in the config file to use in conjuction with `znamutils`
+- `get_children` can work with name or id (instead of id only)
+- `check_flexilims_issues` can now add missing paths
+- `Dataset.from_origin` has a new `extra_attributes` argument to match online datasets
+  with specific attributes only.
+- `delete_recursively` can delete all children of an entity
+- Offline mode using downloaded copy of the database
+
+### Minor
+- `add_mouse` uploads birth and death dates in a human readable format instead.
+- Add `conflicts` argument to `add_mouse` to overwrite existing mice
+- `get_entities` does not raise warnings anymore if `name` is specified and `datatype`
+is not. This is now supported upstream by `flexilims`
+- Clearer error message when mouse info cannot be found in MCMS
+- `load_param` can print the file used to read config with the `verbose` flag.
+
+### Bugfixes
+
+- `update_config` actually adds the new fields (i.e. fields that are in the default
+config but not the local config) to the config file
+
+## v0.3.11
+
+### Bugfixes
+
+- Fix bugs related to raw_data for projects not in main folder
+- Add mouse works with alive animals
+
+
+## v0.3.10
+
+### Main changes
+
+- Make `update_entity` safer by crashing if reserved fields are used as attributes.
+
 ## v0.3.11
 
 ### Bugfixes
@@ -84,6 +125,7 @@ config but not the local config) to the config file
   `return_paths=False`
 - New `OnixData` class to handle Onix data
 - `get_flexilims_session` can now re-use token from a previous session
+- Add a GUI module.
 
 ### Minor
 - More generic `clean_recursively` replaces the `clean_dictionary_recursively`. It
@@ -92,17 +134,19 @@ config but not the local config) to the config file
 - `Dataset.format(mode='yaml')` ensure yaml compatibility. (path to str, tuple to list,
   etc...)
 - `add_experimental_session` can be done with `parent_id` (or `parent_name`).
-- `add_dataset` can add a dataset to a mouse.
-- `get_password` syntax changed to match the `add_password` syntax.
+- `add_dataset` can add a dataset to a mouse and does not require genealogy.
+
 
 ### Bugfixes
 - Fix [#68](https://github.com/znamlab/flexiznam/issues/68). Dataset.format returns
   always the path in posix format.
 - Fix [#88](https://github.com/znamlab/flexiznam/issues/88). Now make attributes JSON
   compatible before uploading to flexilims. This will replace special characters in
   attribute names by `_` in the database.
-- Fix [[#102](https://github.com/znamlab/flexiznam/issues/102). `add_mouse` now works
+- Fix [#102](https://github.com/znamlab/flexiznam/issues/102). `add_mouse` now works
   with mice that have special character in their allele.
+- `add_recording` and `add_sample` add the value online with the full name (including
+  genealogy) rather than the short name.
 
 ## v0.3.4
 

README.md

@@ -38,7 +38,7 @@ To set up the flexilims and mcms integration, the config file must be edited. Fi
 flexiznam config
 ```
 
-This should create a `~/.flexiznam/config.yml` file. Edit it with your favorite text editor to change `flexilims_username`, `mcms_username` and, 
+This should create a `~/.flexiznam/config.yml` file. Edit it with your favorite text editor to change `flexilims_username`, `mcms_username` and,
 if neeed `data_root`.
 
 You can then add passwords to make it simpler by running (one by one):
@@ -78,7 +78,7 @@ If you used `pip -e .` to install, updating can be done with:
 
 ```
 cd flexiznam
-git pull 
+git pull
 pip install -e . --upgrade
 flexiznam config --update
 ```

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -1,68 +1,68 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath("../.."))
-
-# -- Project information -----------------------------------------------------
-
-project = "flexiznam"
-copyright = "2021, Antonin Blot, Petr Znamenskiy"
-author = "Antonin Blot, Petr Znamenskiy"
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosectionlabel",
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.napoleon",
-    "sphinx.ext.viewcode",
-    "sphinx_click",
-]
-
-intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
-    "pandas": ("https://pandas.pydata.org/docs/", None),
-}
-
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "sphinx_rtd_theme"
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+# -- Project information -----------------------------------------------------
+
+project = "flexiznam"
+copyright = "2021, Antonin Blot, Petr Znamenskiy"
+author = "Antonin Blot, Petr Znamenskiy"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_click",
+]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+}
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

docs/source/flexiznam.camp.rst

@@ -8,7 +8,7 @@ Module contents
    :members:
    :undoc-members:
    :show-inheritance:
-   
+
 flexiznam.camp.sync\_data module
 --------------------------------
 

flexiznam/.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+exclude: 'conf.py'
+
+# Configuring https://pre-commit.ci/
+ci:
+    autoupdate_schedule: monthly
+
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+    - repo: https://github.com/psf/black
+      rev: 23.3.0
+      hooks:
+          - id: black
+    - repo: https://github.com/kynan/nbstripout
+      rev: 0.6.1
+      hooks:
+          - id: nbstripout
+            args: [--extra-keys=metadata.language_info.version metadata.kernelspec.name metadata.kernelspec.display_name]